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- EMDB-16036: human MDM2-5S RNP -

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Basic information

Entry
Database: EMDB / ID: EMD-16036
Titlehuman MDM2-5S RNP
Map datahuman MDM2-5S RNP (local filtered map)
Sample
  • Complex: human MDM2-5S RNP
    • Protein or peptide: E3 ubiquitin-protein ligase Mdm2
    • RNA: 5S rRNA
    • Protein or peptide: 60S ribosomal protein L5
    • Protein or peptide: 60S ribosomal protein L11
  • Ligand: ZINC ION
Keywords5S RNP / Mdm2 / RNA BINDING PROTEIN
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / fibroblast activation / Trafficking of AMPA receptors / receptor serine/threonine kinase binding ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / fibroblast activation / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / negative regulation of protein neddylation / peroxisome proliferator activated receptor binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of vascular associated smooth muscle cell migration / negative regulation of protein processing / SUMO transferase activity / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / response to iron ion / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / negative regulation of ubiquitin protein ligase activity / positive regulation of muscle cell differentiation / cardiac septum morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / blood vessel development / SUMOylation of ubiquitinylation proteins / ligase activity / cellular response to alkaloid / Constitutive Signaling by AKT1 E17K in Cancer / regulation of protein catabolic process / negative regulation of signal transduction by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / response to magnesium ion / cellular response to UV-C / Eukaryotic Translation Termination / protein sumoylation / ubiquitin ligase inhibitor activity / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / blood vessel remodeling / cellular response to estrogen stimulus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / protein localization to nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of protein binding / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / protein targeting / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein autoubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / NPAS4 regulates expression of target genes / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription repressor complex / cytosolic ribosome / positive regulation of mitotic cell cycle / regulation of heart rate / proteolysis involved in protein catabolic process / positive regulation of translation / regulation of signal transduction by p53 class mediator / positive regulation of protein export from nucleus / ribosomal large subunit biogenesis / ubiquitin binding / mRNA 3'-UTR binding / response to cocaine / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / establishment of protein localization / Regulation of RUNX3 expression and activity / cellular response to gamma radiation / Oncogene Induced Senescence / RING-type E3 ubiquitin transferase / protein destabilization / Regulation of TP53 Activity through Methylation / mRNA 5'-UTR binding / cellular response to growth factor stimulus / response to toxic substance / centriolar satellite / Regulation of expression of SLITs and ROBOs / cellular response to hydrogen peroxide / protein polyubiquitination / rRNA processing / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / p53 binding / ubiquitin protein ligase activity
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Zinc finger RING-type profile. / Zinc finger, RING-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsCastillo N / Thoms M / Flemming D / Hammaren HM / Buschauer R / Ameismeier M / Bassler J / Beck M / Beckmann R / Hurt E
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)RK1721 Germany
German Research Foundation (DFG)HU363/15-2 Germany
European Research Council (ERC)885711European Union
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways.
Authors: Nestor Miguel Castillo Duque de Estrada / Matthias Thoms / Dirk Flemming / Henrik M Hammaren / Robert Buschauer / Michael Ameismeier / Jochen Baßler / Martin Beck / Roland Beckmann / Ed Hurt /
Abstract: The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is ...The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is disturbed, a free 5S RNP can enter the MDM2-p53 pathway to regulate cell cycle and apoptotic signaling. Here we reconstitute and determine the cryo-electron microscopy structure of the conserved hexameric 5S RNP with fungal or human factors. This reveals how the nascent 5S rRNA associates with the initial nuclear import complex Syo1-uL18-uL5 and, upon further recruitment of the nucleolar factors Rpf2 and Rrs1, develops into the 5S RNP precursor that can assemble into the pre-ribosome. In addition, we elucidate the structure of another 5S RNP intermediate, carrying the human ubiquitin ligase Mdm2, which unravels how this enzyme can be sequestered from its target substrate p53. Our data provide molecular insight into how the 5S RNP can mediate between ribosome biogenesis and cell proliferation.
History
DepositionOct 28, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16036.png

Downloads & links

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Map

FileDownload / File: emd_16036.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman MDM2-5S RNP (local filtered map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211.8 Å		1.06 Å/pix.
x 200 pix.
= 211.8 Å		1.06 Å/pix.
x 200 pix.
= 211.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.05936509 - 0.14046915
Average (Standard dev.)0.0003764116 (±0.0054293275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: human MDM2-5S RNP (post-processed map)

Fileemd_16036_additional_1.map
Annotationhuman MDM2-5S RNP (post-processed map)
Projections & Slices
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Additional map: human MDM2-5S RNP (maked 3D Refinement)

Fileemd_16036_additional_2.map
Annotationhuman MDM2-5S RNP (maked 3D Refinement)
Projections & Slices
AxesZYX

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Histogram

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Additional map: human MDM2-5S RNP (unmaked 3D Refinement)

Fileemd_16036_additional_3.map
Annotationhuman MDM2-5S RNP (unmaked 3D Refinement)
Projections & Slices
AxesZYX

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Histogram

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Half map: human MDM2-5S RNP (maked 3D Refinement, half map 1)

Fileemd_16036_half_map_1.map
Annotationhuman MDM2-5S RNP (maked 3D Refinement, half map 1)
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: human MDM2-5S RNP (maked 3D Refinement, half map 2)

Fileemd_16036_half_map_2.map
Annotationhuman MDM2-5S RNP (maked 3D Refinement, half map 2)
Projections & Slices
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Sample components

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Entire : human MDM2-5S RNP

EntireName: human MDM2-5S RNP
Components
  • Complex: human MDM2-5S RNP
    • Protein or peptide: E3 ubiquitin-protein ligase Mdm2
    • RNA: 5S rRNA
    • Protein or peptide: 60S ribosomal protein L5
    • Protein or peptide: 60S ribosomal protein L11
  • Ligand: ZINC ION

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Supramolecule #1: human MDM2-5S RNP

SupramoleculeName: human MDM2-5S RNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase Mdm2

MacromoleculeName: E3 ubiquitin-protein ligase Mdm2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.293758 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MCNTNMSVPT DGAVTTSQIP ASEQETLVRP KPLLLKLLKS VGAQKDTYTM KEVLFYLGQY IMTKRLYDEK QQHIVYCSND LLGDLFGVP SFSVKEHRKI YTMIYRNLVV VNQQESSDSG TSVSENRCHL EGGSDQKDLV QELQEEKPSS SHLVSRPSTS S RRRAISET ...String:
MCNTNMSVPT DGAVTTSQIP ASEQETLVRP KPLLLKLLKS VGAQKDTYTM KEVLFYLGQY IMTKRLYDEK QQHIVYCSND LLGDLFGVP SFSVKEHRKI YTMIYRNLVV VNQQESSDSG TSVSENRCHL EGGSDQKDLV QELQEEKPSS SHLVSRPSTS S RRRAISET EENSDELSGE RQRKRHKSDS ISLSFDESLA LCVIREICCE RSSSSESTGT PSNPDLDAGV SEHSGDWLDQ DS VSDQFSV EFEVESLDSE DYSLSEEGQE LSDEDDEVYQ VTVYQAGESD TDSFEEDPEI SLADYWKCTS CNEMNPPLPS HCN RCWALR ENWLPEDKGK DKGEISEKAK LENSTQAEEG FDVPDCKKTI VNDSRESCVE ENDDKITQAS QSQESEDYSQ PSTS SSIIY SSQEDVKEFE REETQDKEES VESSLPLNAI EPCVICQGRP KNGCIVHGKT GHLMACFTCA KKLKKRNKPC PVCRQ PIQM IVLTYFP

UniProtKB: E3 ubiquitin-protein ligase Mdm2

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Macromolecule #3: 60S ribosomal protein L5

MacromoleculeName: 60S ribosomal protein L5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.426789 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGFVKVVKNK AYFKRYQVKF RRRREGKTDY YARKRLVIQD KNKYNTPKYR MIVRVTNRDI ICQIAYARIE GDMIVCAAYA HELPKYGVK VGLTNYAAAY CTGLLLARRL LNRFGMDKIY EGQVEVTGDE YNVESIDGQP GAFTCYLDAG LARTTTGNKV F GALKGAVD ...String:
MGFVKVVKNK AYFKRYQVKF RRRREGKTDY YARKRLVIQD KNKYNTPKYR MIVRVTNRDI ICQIAYARIE GDMIVCAAYA HELPKYGVK VGLTNYAAAY CTGLLLARRL LNRFGMDKIY EGQVEVTGDE YNVESIDGQP GAFTCYLDAG LARTTTGNKV F GALKGAVD GGLSIPHSTK RFPGYDSESK EFNAEVHRKH IMGQNVADYM RYLMEEDEDA YKKQFSQYIK NSVTPDMMEE MY KKAHAAI RENPVYEKKP KKEVKKKRWN RPKMSLAQKK DRVAQKKASF LRAQERAAES

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #4: 60S ribosomal protein L11

MacromoleculeName: 60S ribosomal protein L11 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.288465 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MAQDQGEKEN PMRELRIRKL CLNICVGESG DRLTRAAKVL EQLTGQTPVF SKARYTVRSF GIRRNEKIAV HCTVRGAKAE EILEKGLKV REYELRKNNF SDTGNFGFGI QEHIDLGIKY DPSIGIYGLD FYVVLGRPGF SIADKKRRTG CIGAKHRISK E EAMRWFQQ KYDGIILPGK

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #2: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.951105 KDa
SequenceString:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGG UGACCAUACG CGAAACUCAG GUGCUGCAAU CU

GENBANK: GENBANK: CP008196.1

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219620
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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